HOW COMMON IS HOMOPLOID HYBRID SPECIATION?

Hybridization has long been considered a process that prevents divergence between species. In contrast to this historical view, an increasing number of empirical studies claim to show evidence for hybrid speciation without a ploidy change. However, the importance of hybridization as a route to speciation is poorly understood, and many claims have been made with insufficient evidence that hybridization played a role in the speciation process. We propose criteria to determine the strength of evidence for homoploid hybrid speciation. Based on an evaluation of the literature using this framework, we conclude that although hybridization appears to be common, evidence for an important role of hybridization in homoploid speciation is more circumscribed.     

HOW MANY SPECIES OF ALGAE ARE THERE?

Algae have been estimated to include anything from 30,000 to more than 1 million species. An attempt is made here to arrive at a more accurate estimate using species numbers in phyla and classes included in the on‐line taxonomic database AlgaeBase ( http://www.algaebase.org ). Despite uncertainties regarding what organisms should be included as algae and what a species is in the context of the various algal phyla and classes, a conservative approach results in an estimate of 72,500 algal species, names for 44,000 of which have probably been published, and 33,248 names have been processed by AlgaeBase to date (June 2012). Some published estimates of diatom numbers are of over 200,000 species, which would result in four to five diatom species for every other algal species. Concern is expressed at the decline and potential extinction of taxonomists worldwide capable of improving and completing the necessary systematic studies.     

ESTIMATING DIVERSIFICATION RATES: HOW USEFUL ARE DIVERGENCE TIMES?

The dynamics of species diversification rates are a key component of macroevolutionary patterns. Although not absolutely necessary, the use of divergence times inferred from sequence data has led to development of more powerful methods for inferring diversification rates. However, it is unclear what impact uncertainty in age estimates have on diversification rate inferences. Here, we quantify these effects using both Bayesian and frequentist methodology. Through simulation, we demonstrate that adding sequence data results in more precise estimates of internal node ages, but a reasonable approximation of these node ages is often sufficient to approach the theoretical minimum variance in speciation rate estimates. We also find that even crude estimates of divergence times increase the power of tests of diversification rate differences between sister clades. Finally, because Bayesian and frequentist methods provided similar assessments of error, novel Bayesian approaches may provide a useful framework for tests of diversification rates in more complex contexts than are addressed here.     

HOW ARE DELETERIOUS MUTATIONS PURGED? DRIFT VERSUS NONRANDOM MATING

Accumulation of deleterious mutations has important consequences for the evolution of mating systems and the persistence of small populations. It is well established that consanguineous mating can purge a part of the mutation load and that lethal mutations can also be purged in small populations. However, the efficiency of purging in natural populations, due to either consanguineous mating or to reduced population size, has been questioned. Consequences of consanguineous mating systems and small population size are often equated under "inbreeding" because both increase homozygosity, and selection is though to be more efficient against homozygous deleterious alleles. I show that two processes of purging that I call "purging by drift" and "purging by nonrandom mating" have to be distinguished. Conditions under which the two ways of purging are effective are derived. Nonrandom mating can purge deleterious mutations regardless of their dominance level, whereas only highly recessive mutations can be purged by drift. Both types of purging are limited by population size, and sharp thresholds separate domains where purging is either effective or not. The limitations derived here on the efficiency of purging are compatible with some experimental studies. Implications of these results for conservation and evolution of mating systems are discussed.     

THE CLASSIFICATION OF PROBOSCIDEA: HOW MANY CLADISTIC CLASSIFICATIONS?

Abstract— Hennig conceived a method to build a "phylogenetic system", with the stipulation that a "properly drawn phylogenetic tree must be directly translatable into the language of phylogenetic systematics". Consequently, this system could be the general reference system of biology. A review of the classificatory technical improvements, conventions and rules which have been proposed for the past twenty years together with their application to the classification of the Proboscidea, leads to the conclusion that more than one formal system can be built upon one given cladogram. As words are used more frequently for communication than diagrams, schemes or graphs, the "general reference system of biology1' remains somewhere in Utopia. The "phylogenetic system" is rather more synonymous with a cladogram than with a written classification.     

HOW DOES POLLEN VERSUS SEED DISPERSAL AFFECT NICHE EVOLUTION?

In heterogeneous landscapes, the genetic and demographic consequences of dispersal influence the evolution of niche width. Unless pollen is limiting, pollen dispersal does not contribute directly to population growth. However, by disrupting local adaptation, it indirectly affects population dynamics. We compare the effect of pollen versus seed dispersal on the evolution of niche width in heterogeneous habitats, explicitly considering the feedback between maladaptation and demography. We consider two scenarios: the secondary contact of two subpopulations, in distinct, formerly isolated habitats, and the colonization of an empty habitat with dispersal between the new and ancestral habitat. With an analytical model, we identify critical levels of genetic variance leading to niche contraction (secondary contact scenario), or expansion (new habitat scenario). We confront these predictions with simulations where the genetic variance freely evolves. Niche contraction occurs when habitats are very different. It is faster as total gene flow increases or as pollen predominates in overall gene flow. Niche expansion occurs when habitat heterogeneity is not too high. Seed dispersal accelerates it, whereas pollen dispersal tends to retard it. In both scenarios very high seed dispersal leads to extinction. Overall, our results predict a wider niche for species dispersing seeds more than pollen.     

COMPARING STRENGTHS OF DIRECTIONAL SELECTION: HOW STRONG IS STRONG?

The fundamental equation in evolutionary quantitative genetics, the Lande equation, describes the response to directional selection as a product of the additive genetic variance and the selection gradient of trait value on relative fitness. Comparisons of both genetic variances and selection gradients across traits or populations require standardization, as both are scale dependent. The Lande equation can be standardized in two ways. Standardizing by the variance of the selected trait yields the response in units of standard deviation as the product of the heritability and the variance-standardized selection gradient. This standardization conflates selection and variation because the phenotypic variance is a function of the genetic variance. Alternatively, one can standardize the Lande equation using the trait mean, yielding the proportional response to selection as the product of the squared coefficient of additive genetic variance and the mean-standardized selection gradient. Mean-standardized selection gradients are particularly useful for summarizing the strength of selection because the mean-standardized gradient for fitness itself is one, a convenient benchmark for strong selection. We review published estimates of directional selection in natural populations using mean-standardized selection gradients. Only 38 published studies provided all the necessary information for calculation of mean-standardized gradients. The median absolute value of multivariate mean-standardized gradients shows that selection is on average 54% as strong as selection on fitness. Correcting for the upward bias introduced by taking absolute values lowers the median to 31%, still very strong selection. Such large estimates clearly cannot be representative of selection on all traits. Some possible sources of overestimation of the strength of selection include confounding environmental and genotypic effects on fitness, the use of fitness components as proxies for fitness, and biases in publication or choice of traits to study.     

THE LOCI OF EVOLUTION: HOW PREDICTABLE IS GENETIC EVOLUTION?

Is genetic evolution predictable? Evolutionary developmental biologists have argued that, at least for morphological traits, the answer is a resounding yes. Most mutations causing morphological variation are expected to reside in the cis‐regulatory, rather than the coding, regions of developmental genes. This “cis‐regulatory hypothesis” has recently come under attack. In this review, we first describe and critique the arguments that have been proposed in support of the cis‐regulatory hypothesis. We then test the empirical support for the cis‐regulatory hypothesis with a comprehensive survey of mutations responsible for phenotypic evolution in multicellular organisms. Cis‐regulatory mutations currently represent approximately 22% of 331 identified genetic changes although the number of cis‐regulatory changes published annually is rapidly increasing. Above the species level, cis‐regulatory mutations altering morphology are more common than coding changes. Also, above the species level cis‐regulatory mutations predominate for genes not involved in terminal differentiation. These patterns imply that the simple question “Do coding or cis‐regulatory mutations cause more phenotypic evolution?” hides more interesting phenomena. Evolution in different kinds of populations and over different durations may result in selection of different kinds of mutations. Predicting the genetic basis of evolution requires a comprehensive synthesis of molecular developmental biology and population genetics.     

HOW AND WHEN DO LAMBS RECOGNIZE THE BLEATS OF THEIR MOTHERS?

ABSTRACT

In domestic sheep Ovis aries, the mother and the young display a preferential bond for each other that relies on multimodal inter-individual recognition. Lambs show a preference for their own dam shortly after birth, and this is important for their survival. The role of acoustic cues in this early preference for the mother is not clear. The aim of the present work was to analyze the timing of acoustic recognition of the mother and to identify the physical parameters used in the recognition of maternal bleats by the lamb.

In a first study, we investigated the ability of lambs to discriminate between the bleats of their own mother and an alien equivalent mother in a two-choice test. Both ewes were hidden behind a canvas sheet and lambs were not allowed to approach the dams closer than 1 m, thus preventing visual as well as olfactory perception. Tests were conducted 12 hr, 24 hr or 48 hr after birth (n=19 or 20/group). An indication of vocal discrimination was already present at 24 hr and at 48 hr lambs spent significantly more time near their mother than near the alien dam.

In a second step, we investigated which physical parameters of the bleats were important for recognition. For this, we conducted playback experiments with modified bleats at two weeks postpartum. Ours results show that lambs pay attention to a combination of various time, energy and frequency parameters: timbre (distribution of energy within the spectrum), amplitude and frequency modulations appear to be the most important parameters encoding the individual signature.

We conclude that vocal recognition between the ewe and her lamb plays an important role in the display of preferential mother-young bond from very early on. Our studies also demonstrate that the encoding of the individual signature is not limited to the frequency domain but rather involves a multiparametric encoding process.     

EVOLUTIONARY RESPONSES TO ENVIRONMENTAL CHANGES: HOW DOES COMPETITION AFFECT ADAPTATION?

The role and importance of ecological interactions for evolutionary responses to environmental changes is to large extent unknown. Here it is shown that interspecific competition may slow down rates of adaptation substantially and fundamentally change patterns of adaptation to long-term environmental changes. In the model investigated here, species compete for resources distributed along an ecological niche space. Environmental change is represented by a slowly moving resource maximum and evolutionary responses of single species are compared with responses of coalitions of two and three competing species. In scenarios with two and three species, species that are favored by increasing resource availability increase in equilibrium population size whereas disfavored species decline in size. Increased competition makes it less favorable for individuals of a disfavored species to occupy a niche close to the maximum and reduces the selection pressure for tracking the moving resource distribution. Individual-based simulations and an analysis using adaptive dynamics show that the combination of weaker selection pressure and reduced population size reduces the evolutionary rate of the disfavored species considerably. If the resource landscape moves stochastically, weak evolutionary responses cause large fluctuations in population size and thereby large extinction risk for competing species, whereas a single species subject to the same environmental variability may track the resource maximum closely and maintain a much more stable population size. Other studies have shown that competitive interactions may amplify changes in mean population sizes due to environmental changes and thereby increase extinction risks. This study accentuates the harmful role of competitive interactions by illustrating that they may also decrease rates of adaptation. The slowdown in evolutionary rates caused by competition may also contribute to explain low rates of morphological change in spite of large environmental fluctuations found in fossil records.     

Tissue development and RNA control: "HOW" is it coordinated?

The regulation of developmental processes at the RNA level enables selective and rapid modulation of gene expression. Studies in model organisms revealed the essential contribution of the signal transduction and activation of RNA (STAR) family of RNA binding proteins to developmental processes. STAR proteins coordinate the proper timing of developmental events by delaying expression or altering the mRNA or protein levels of essential genes. Recent functional analysis of the Drosophila melanogaster STAR protein, Held Out Wing (HOW), in the context of embryonic development, provided insight into its mode of activity. Here, we describe HOW's activity in the temporal repression or elevation of gene expression that is essential for coordinating the correct timing of instructive signals.     

HOW DOES SPATIAL DISPERSAL NETWORK AFFECT THE EVOLUTION OF PARASITE LOCAL ADAPTATION?

Studying patterns of parasite local adaptation can provide insights into the spatiotemporal dynamics of host–parasite coevolution. Many factors, both biotic and abiotic, have been identified that influence parasite local adaptation. In particular, dispersal and population structuring are considered important determinants of local adaptation. We investigated how the shape of the spatial dispersal network within experimental landscapes affected local adaptation of a bacteriophage parasite to its bacterial host. Regardless of landscape topology, dispersal always led to the evolution of phages with broader infectivity range. However, when the spatial dispersal network resulted in spatial variation in the breadth of phage infectivity range, significant levels of parasite local adaptation and local maladaptation were detected within the same landscape using the local versus foreign definition of local adaptation. By contrast, local adaptation was not detected using the home versus away or local versus global definitions of local adaptation. This suggests that spatial dispersal networks may play an important role in driving parasite local adaptation, particularly when the shape of the dispersal network generates nonuniform levels of host resistance or parasite infectivity throughout a species’ range.     

WHERE AM I? HOW A CELL RECOGNIZES ITS POSITIONAL INFORMATION DURING MORPHOGENESIS

Morphogenesis is an old, and one of the latest, fascinating fields in biological science and a huge number of papers on molecular mechanisms underlying it have been published. But most of the works and reviews on these mechanisms pertain to molecules of, as it were, the planning or design of morphogenesis, such as morphogens and homeodomain proteins. In this review, I will describe the function of extracellular matrix (ECM) and other cell adhesion molecules in morphogenesis as that of actual morpho-creating molecules, morphocreators, and discuss their roles as positional information-pertaining molecules.     

HOW DEPRESSED? ESTIMATES OF INBREEDING EFFECTS DURING SEED DEVELOPMENT DEPEND ON REPRODUCTIVE CONDITIONS

Inbreeding depression can reduce the performance of offspring produced by mating between relatives, with consequences for population dynamics and sexual-system evolution. In flowering plants, inbreeding depression commonly acts most intensely during seed development. This predispersal component is typically estimated by comparing seed production following exclusive self- and cross-pollination, but such estimates are unbiased only if seed production is limited by ovule availability, rather than by pollen receipt or seed-development resources. To overcome this problem, we propose experimental and statistical methods based on a model of ovule fertilization and seed development that accounts for differential fertilization by self- and cross-pollen, limited ovule viability or receptivity, differential survival of self- and cross-zygotes and limited resource availability. Simulations illustrate that the proposed methods eliminate bias in estimated predispersal inbreeding depression caused by pollen limitation and can improve estimates under resource limitation. Application of these methods to two orchid species further demonstrates their utility in identifying and estimating diverse influences on reproductive performance under typical conditions. Although our theoretical results raise questions about the reported intensity of predispersal inbreeding depression, our proposed methods guard against bias while also providing insight into plant reproduction.     

SPERM‐LIMITED FECUNDITY IN NEMATODES: HOW MANY SPERM ARE ENOUGH?

The Bateman principle, which holds that oocytes are the limiting gamete in reproduction, is violated in a variety of species. Self-fertilizing hermaphrodites of the nematode Caenorhabditis elegans provide an example of a system in which sperm number limits lifetime reproductive output, in this species due to the protandrous nature of sperm production that in turn delays the onset of fertilization. This reproductive delay forms the basis of a trade-off between generation time and total fecundity, in which sperm number plays a pivotal role. I use an age-structured population model to describe the number of sperm that maximize fitness, given larval development time and rates of gamete production. The model predicts the evolution of sperm numbers that are consistent with empirical data for C. elegans provided that precocious larval sperm production is taken into account. Several testable hypotheses follow from the model regarding how natural selection and environmental variation may influence patterns of sperm production among populations or species with a similar mode of reproduction.     

THE PLACE OF GOD IN SYNTHETIC BIOLOGY: HOW WILL THE CATHOLIC CHURCH RESPOND?

Some religious believers may see synthetic biology as usurping God's creative role. The Catholic Church has yet to issue a formal teaching on the field (though it has issued some informal statements in response to Craig Venter's development of a 'synthetic' cell). In this paper I examine the likely reaction of the Catholic Magisterium to synthetic biology in its entirety. I begin by examining the Church's teaching role, from its own viewpoint, to set the necessary backround and context for the discussion that follows. I then describe the Church's attitude to science, and particularly to biotechnology. From this I derive a likely Catholic theology of synthetic biology. The Church's teachings on scientific and biotech research show that it is likely to have a generally positive disposition to synbio, if it and its products can be acceptably safe. Proper evaluation of, and protection against, risk will be a significant factor in determining the morality of the research. If the risks can be minimized through regulation or other means, then the Church is likely to be supportive. The Church will also critique the social and legal environment in which the research is done, evaluating issues such as the patenting of scientific discoveries and of life.     

HOW WELL DOES THE 9‐POINT HEDONIC SCALE PREDICT PURCHASE FREQUENCY?

One hundred and one consumers assessed three strawberry‐flavored yogurts, using the 9‐point hedonic scale and a purchase intent scale, both blind and with their appropriate cartons. They were then monitored for a year, to determine whether their ratings had any predictive value for their purchase behavior. It was found that the highest rated yogurts tended to be the ones that were purchased during the year. Any correspondence between rank order of rating and of purchase frequency was negligible. Predictions were better when the yogurts were rated with their cartons. The ratings were a better predictor of purchase frequency than price. Various consistency measures were also made.     

ESTIMATION OF TOTAL BODY WATER IN HARBOR SEALS: HOW USEFUL IS BIOELECTRICAL IMPEDANCE ANALYSIS?

We evaluated bioelectrical impedance analysis (BIA) as a means of rapidly and inexpensively estimating total body water (TBW) of harbor seals ( Phoca vitulina ). Deuterium oxide dilution was used to estimate TBW in 17 adult females and 16 of their pups between birth and late lactation. Isotope dilution was also used to determine TBW in 12 adult males early and 10 of these males late in the breeding season. At the same time, resistance ( Rs ) and reactance ( Xc ) measurements were taken using a tetrapolar, impedance plethysmograph (Model 101 A, RJL Systems). Seals were sedated with diazepam prior to taking BIA measurements. Within-day duplicate Rs measurements on pups and adults, taken 2-240 min apart, differed by an average of 3.0%± 1.4% ( n = 42, CV = 102%). Movement of the seal during BIA measurements caused variability in both Rs and Xc values. BIA measurements were generally poor predictors of TBW. Rs was significantly correlated with TBW in pups only ( Rs = 0.93, P = 0.001, n = 11). Bioelectrical conductor volume (length2/ Rs ) was significantly correlated with TBW only in adult females ( Rs = 0.63, P = 0.02, n = 14). We conclude that BIA is not a reliable method of estimating TBW in wild harbor seals.